Runs Yushkevich's ASHS, built on ubuntu:24.04, with embedded ASHS UPENN PMC atlas.
953
Source of binaries: https://sites.google.com/view/ashs-dox/home
Runs automated hippocampal subfield segmentation (ASHS) using T1- and T2-weighted files. Bootstrap skipped (-B). Uses UPenn PMC Atlas by default, accepts reference to other atlases.
Required Arguments:
-v </path>:/t1_dir = directory containing T1w file
-v </path>:/t2_dir = directory containing T2w file
-v </path>:/work_dir = derivatives output directory
-i <str> = subject name
-g <str> = file name of T1w NIfTI
-f <str> = file name of T2w NIfTI
Optional Arguments:
-a <str> = atlas name, requires binding of parent directory
Example Usage:
docker run \
-v /home/data/dset/sub-1234/ses-A/anat:/t1_dir \
-v /home/data/dset/sub-1234/ses-A/anat:/t2_dir \
-v /home/data/derivatives/ashs/sub-1234/ses-A:/work_dir \
nmuncy/ashs \
-i sub-1234 \
-g sub-1234_ses-A_T1w.nii.gz \
-f sub-1234_ses-A_T2w.nii.gz
docker run \
-v /home/data/dset/sub-1234/ses-A/anat:/t1_dir \
-v /home/data/dset/sub-1234/ses-A/anat:/t2_dir \
-v /home/data/derivatives/ashs/sub-1234/ses-A:/work_dir \
-v /home/atlases:/atlas_dir \
nmuncy/ashs \
-i sub-1234 \
-g sub-1234_ses-A_T1w.nii.gz \
-f sub-1234_ses-A_T2w.nii.gz \
-a ashs_atlas_magdeburg
Content type
Image
Digest
sha256:fb3c30f2e…
Size
3.5 GB
Last updated
over 1 year ago
docker pull nmuncy/ashs